Qiime2 import error

Hi,
I am using this command
qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path /media/moloy/LaCie/bburg/expt2/pool1/alldemulti/manifest.csv --output-path demux_import.qza
There was a problem importing /media/moloy/LaCie/bburg/expt2/pool1/alldemulti/manifest.csv:

Then qiime2 complains :tired_face:
Importing ‘SingleLanePerSamplePairedEndFastqDirFmt’ requires a directory, not /media/moloy/LaCie/bburg/expt2/pool1/alldemulti/manifest.csv
what is wrong here. Can anyone help.

Hi @amit,
Looks like you are trying to import using the manifest format but you’re just missing one extra parameter. Try this:

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path /media/moloy/LaCie/bburg/expt2/pool1/alldemulti/manifest.csv \
  --output-path demux_import.qza \
  --input-format PairedEndFastqManifestPhred64 

Was just missing the last --input-format. Note, that if you are using a version of qiime2 older than 2018.8, then replace --input-format with --source-format

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Hi @Mehrbod_Estaki I tried but it does work and complains -

There was a problem importing /media/moloy/LaCie/bburg/expt2/pool1/alldemulti/manifest_1.csv:
/media/moloy/LaCie/bburg/expt2/pool1/alldemulti/manifest_1.csv is not a(n) PairedEndFastqManifestPhred64 file
The manifest file that I am using is attached. I have no clue why it is giving me an error. Kindly have a look.manifest_1.csv (1.5 KB)

Hi @Mehrbod_Estaki,
I removed the double quotes and executed the code-
qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path /media/moloy/LaCie/bburg/expt2/pool1/alldemulti/manifest.csv --output-path demux_import.qza --input-format PairedEndFastqManifestPhred33
It worked ! Thanks for your support.

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